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annotate samtools_calmd.xml @ 4:06dc50b7b711 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_calmd commit 851f81495c875ac09d936537ffd2b32e6af2c8c5"
author iuc
date Thu, 17 Oct 2019 02:18:43 -0400
parents 3d873744df7e
children c147e3a10573
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1 <tool id="samtools_calmd" name="CalMD" version="2.0.2">
1
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2 <description>recalculate MD/NM tags</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="requirements"/>
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7 <expand macro="stdio"/>
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8 <expand macro="version_command"/>
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9 <command><![CDATA[
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10 @ADDTHREADS@
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11 #if str( $reference_source.reference_source_selector ) == "history":
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12 #set ref_fa = 'ref.fa'
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13 ln -s '${reference_source.ref_fasta}' ref.fa &&
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14 samtools faidx ref.fa &&
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15 #else:
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16 #set ref_fa = str( $reference_source.ref_fasta.fields.path )
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17 #end if
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18
3
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19 samtools calmd
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20 $baq_settings.use_baq $baq_settings.modify_quality $baq_settings.extended_baq
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21 #if str($option_set.option_sets) == 'advanced':
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22 $option_set.change_identical -C $option_set.adjust_mq
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23 #end if
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24 -b
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25 -@ \$addthreads
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26 '$input_bam'
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27 '$ref_fa'
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28 > '$calmd_output'
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29 ]]></command>
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30 <inputs>
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31 <param name="input_bam" type="data" format="bam" label="BAM file to recalculate" />
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32 <conditional name="reference_source">
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33 <param name="reference_source_selector" type="select" label="Choose the source for the reference genome">
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34 <option value="cached">Use a built-in genome</option>
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35 <option value="history">Use a genome from the history</option>
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36 </param>
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37 <when value="cached">
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38 <param name="ref_fasta" type="select" label="Using reference genome">
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39 <options from_data_table="fasta_indexes">
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40 <filter type="data_meta" column="dbkey" key="dbkey" ref="input_bam" />
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41 <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file" />
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42 </options>
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43 </param>
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44 </when>
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45 <when value="history">
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46 <param name="ref_fasta" type="data" format="fasta" label="Using reference file" />
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47 </when>
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48 </conditional>
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49 <conditional name="baq_settings">
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50 <param name="use_baq" argument="-r" type="select"
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51 label="Do you also want BAQ (Base Alignment Quality) scores to be calculated?">
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52 <option value="">No</option>
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53 <option value="-r">Yes, run BAQ calculation</option>
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54 </param>
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55 <when value="">
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56 <param name="modify_quality" type="hidden" value="" />
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57 <param name="extended_baq" type="hidden" value="" />
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58 </when>
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59 <when value="-r">
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60 <param name="modify_quality" argument="-A" type="boolean" truevalue="-A" falsevalue="" checked="false"
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61 label="Use BAQ to cap read base qualities"
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62 help="By default, BAQ scores are stored in a separate BQ tag, and the read base quality string is left untouched. When you enable this option, the BAQ scores will be used directly to modify the quality string instead." />
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63 <param name="extended_baq" argument="-E" type="boolean" truevalue="-E" falsevalue="" checked="false" label="Extended BAQ for better sensitivity" />
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64 </when>
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65 </conditional>
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66 <conditional name="option_set">
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67 <param name="option_sets" type="select" label="Additional options">
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68 <option value="default">Use defaults</option>
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69 <option value="advanced">Advanced options</option>
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70 </param>
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71 <when value="default" />
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72 <when value="advanced">
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73 <param name="change_identical" argument="-e" type="boolean" truevalue="-e" falsevalue="" checked="False"
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74 label="Change identical bases to '='"
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75 help="Replace bases in read sequences that match the reference base at that position with an equal sign" />
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76 <param name="adjust_mq" argument="-C" type="integer" min="0" max="255" value="0"
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77 label="Coefficient to cap mapping quality of poorly mapped reads"
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78 help="Higher values for this setting mean a stronger downgrade of the mapping quality of reads with excessive mismatches (50: recommended setting for reads aligned with BWA, 0: do not downgrade mapping qualities)" />
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79 </when>
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80 </conditional>
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81 </inputs>
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82 <outputs>
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83 <data name="calmd_output" format="bam" label="${tool.name} on ${on_string}" />
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84 </outputs>
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85 <tests>
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86 <test>
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87 <param name="use_baq" value="" />
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88 <param name="option_sets" value="default" />
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89 <param name="input_bam" value="phiX.bam"/>
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90 <param name="reference_source_selector" value="history" />
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91 <param name="ref_fasta" value="phiX.fasta" />
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92 <output name="calmd_output" file="samtools_calmd_out_1.bam" ftype="bam" />
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93 </test>
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94 <test>
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95 <param name="use_baq" value="-r" />
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96 <param name="extended_baq" value="true" />
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97 <param name="option_sets" value="advanced" />
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98 <param name="change_identical" value="true" />
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99 <param name="adjust_mq" value="50" />
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100 <param name="input_bam" value="phiX.bam"/>
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101 <param name="reference_source_selector" value="history" />
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102 <param name="ref_fasta" value="phiX.fasta" />
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103 <output name="calmd_output" file="samtools_calmd_out_2.bam" ftype="bam" />
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104 </test>
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105 </tests>
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106 <help><![CDATA[
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107 **What it does**
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108
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109 Generates the MD tag using the ``samtools calmd`` command. If the MD tag (see
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110 SAM format reference below for explanation of SAM/BAM tags) is already present,
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111 this command will give a warning if the MD tag generated is different from the
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112 existing tag.
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113
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114 Optionally, also generates the BQ tag to encode base alignment qualities,
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115 caps the mapping quality of poorly mapping reads, and modifies read sequences
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116 replacing bases matching the reference with ``=``.
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117
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118 Outputs a BAM file.
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119
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120 -----
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121
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122 **SAM/BAM tags written by this tool**
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123
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124 From the SAM format tag specification::
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125
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126 MD (string) String for mismatching positions. Regex : [0-9]+(([A-Z]|\^[A-Z]+)[0-9]+)*7
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127 NM (integer) Edit distance to the reference, including ambiguous bases but excluding clipping
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128 BQ (string) String of offsets to base alignment quality (BAQ), of the same length as the read sequence.
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129 At the i-th read base, BAQ i = Q i − (BQ i − 64) where Q i is the i-th base quality.
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130
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131 See references for more information about SAM format tags.
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132 ]]></help>
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133 <expand macro="citations"/>
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134 </tool>